class: center, middle, inverse, title-slide .title[ # Open Science <br>in MARVLS ] .author[ ### Eva Schemmel <br>NOAA Fisheries ] .date[ ### 2023-05-01 ] --- layout: true .footnote[U.S. Department of Commerce | National Oceanic and Atmospheric Administration | National Marine Fisheries Service] --- ## What & Why -- What: Open and available science. -- Why: * Repeatable - future self and others -- * Efficient - don't reinvent the wheel -- * Collaborative - multiple people can work on the same documents and project -- * Version control - can eliminate "doc_final_final.doc" --- ## Barriers to Entry The myths I tell myself: * I am not a good enough coder * There are errors in my analysis that will be discovered * I don't know the programs/github well enough * NOAA policies prevent me from joining in -> actuality NOAA Open Science mandates --- ## Open Science State of Mind * [Openscapes Slides](https://docs.google.com/presentation/d/1giEW0EIYVnxneGpOBSJnEqg-1CVBUGrbH8Z5gawdeBc/edit#slide=id.p) -- * Reframe your work as a collaborative effort not a individual burden -- * Redefine collaborators & community – Future You, Future Us - New perspectives, tools, methods, ideas, colleagues, allies -- * Reimagine challenges – expect there is a better way - Reuse not reinvent: reduce lonely struggles & cognitive load -- * Open as a daily practice - efficient, collaborative, inclusive, kind - Share imperfect work, have empathy, learn & teach together - Requires trust and time: slow down to speed up --- ## Tools & Learning Groups Make it Possible  Openscapes image --- ## Where to Begin * [NMFS Openscapes GitHub org](https://github.com/nmfs-openscapes/.github/wiki) - training resources - NOAA policies and instructions for setting up NOAA github account - links to NOAA open science mandates <img src="data:image/png;base64,#githubstart.png" width="70%" /> --- ## Tools & Resources Available * [RVerse Tutorials](https://rverse-tutorials.github.io/) -Eli Homes' website and repo for everything R and github (and more) * [Openscapes](https://www.openscapes.org/) -[Cohorts - science centers and group shared learning](https://drive.google.com/drive/folders/10MykRskNoP4E0YCwup8rzIeZVm2gA3fO) -Julia Lowndes (julia@openscapes.org) * [NMFS R user group](https://nmfs-opensci.github.io/NMFS-R-UG/) -For information on upcoming meetings and resources * [NMFS Openscience Repo](https://github.com/orgs/nmfs-opensci/repositories) -Github guide -Quarto simple website template -Quarto report -Xaringan presentation (template used for this presentation) * [NOAA Fisheries Toolbox](https://noaa-fisheries-integrated-toolbox.github.io/) -Kathryn Doering (kathryn.doering@noaa.gov ) --- ## Openscience Products: Repeatable Reports .left-column[ * [R Markdown Biosampling Inventory Report](https://repository.library.noaa.gov/view/noaa/45018) -Three Regions -Hundreds of Species -Updated Annually - [Github Repo](https://github.com/NOAA-LHP/Biosampling-Inventory) ] .right-column[ <img src="data:image/png;base64,#temp.png" width="80%" /> ] --- ## Openscience Products: Supplementary Files for Publications * Analysis [Schemmel & Dahl 2023](https://github.com/MARVLS/Fish-Gonad-Staging/tree/main/analyses/Variola_louti_Schemmel_2023) * Full publication: https://doi.org/10.1007/s10641-023-01411-3 <img src="data:image/png;base64,#valo_pub.png" width="60%" /> --- ## Openscience Products: Supplementary Files for Publications * Gonad Macroscopic Images [McBride 2022 - Wolffish ](https://github.com/MARVLS/Fish-Gonad-Staging/tree/main/analyses/) * Full publication: https://doi.org/10.1002/mcf2.10222 <img src="data:image/png;base64,#wolffish.png" width="100%" /> --- ## Openscience Products: Websites * [Simple website template](https://github.com/nmfs-opensci/NOAA-distill-website)  * [New quarto template available](https://github.com/nmfs-opensci/NOAA-quarto-simple) --- ## MARVLS Community * Hold meetings and workshops * standardize methodology * share accomplishments and challenges * provide mentorship * increase collaboration among scientists --- ## MARVLS Websites & Github Organization * [MARVLS Website]() Organize quarterly workshops and share MARVLS content * [MARVLS Learning Center]() Share code and analysis, recent MARVLS papers, fish developmental sequences, histology interpretation, stains, etc * NOAA policy approved - policies enforced differently at each science center  --- ## How to Contribute 1 MARVLS repository membership! .left-column[ [Please use issues for requesting changes to content](https://github.com/MARVLS/MARVLS/issues) * Request change to text or report a typo * Request format change ] .right-column[ .hand-blue[  ] ] --- ## How to Contribute 2 .left-column[ [Add Analyses ](https://github.com/MARVLS/Fish-Gonad-Staging/tree/main/analyses) * Add R code for reproduction assessments here * Use Pull Requests ] .right-column[ .hand-blue[  ] ] --- ## How to Contribute 3 [Add New Content ](https://docs.google.com/spreadsheets/d/1uC-vGAvOSiUSke6Y5pjCHCtO8hYK2HbuVZVa9b2t2p8/edit?usp=share_link) * [Shared Drive -Contribute](https://drive.google.com/drive/u/0/folders/1YeBkEyTUlrrj5RuktUUJJ42J0cS9t_Vp) * Suggest new content * Use google sheet * Add the files that are not available online into the "Contributions" folder  --- ## Histology Reference Template .left-column[ [A template to document developmental sequences.](https://docs.google.com/presentation/d/1l6yKgd4srDlrYsEKtlQsRh-1FmZTicOrgmigT4Az-lo/edit#slide=id.p3) * This template is useful for teaching and provides additional details that make them great references. ] .right-column[ .hand-blue[  ] ] --- ## Discussion Prompts * Is there an openscience standard or best practices for life history and reproductive biology? * What changes are you seeing in our discipline? * How do we (MARVLS) share and work together currently? * How can we improve sharing and learning as a group? * What are your barriers and is there something as a group we can do?